1.1.37 (2017_12_14)

Code generator is now runnable/installable as a standalone tool (named fbgen); and has been verified to work for GTEX portal

Client bindings version discernable via new client_version() endpoint, in both fbget cli tool and firebrowse module; this supplements the longstanding version info embedded within -v CLI option and heartbeat() endpoint

High level endpoints can now be invoked at CLI with 'help' to obtain same help that has historically been available by invoking endpoints with zero arguments

1.1.36 (2017_08_21)

Added OLD RUNS link to top-level menu, so users can quickly contrast legacy run results with what FireBrowse currently displays

The gene parameter is now mandatory for the Samples/mRNASeq API: calling with just a barcode is no longer supported

Likewise, the mir parameter is now mandatory for the Samples/miRSeq API

Python/UNIX client bindings:

Increased value of page_size parameter used internally from the API default of 250 records per page to 1000. The original value of 250 yields a more responsive and robust experience in browsers, but is needlessly low for the programmatic use case where throughput of completing the entire query is a more important than conserving size.

Expose page_size parameter as top-level parameter to fbget: can then be used for any other API call without needing to specify

Which makes it extremely easy to determine for what patients and cohorts any given CDE is defined: e.g.fbget clinical cde=gleason_scorewill show each patient case with a valid gleason_score, across all cohorts

viewGene: now enforces rendering of at most 1 gene per Submit; if multiple genes are given the first is selected

iCoMut:

Popup tooltips for mutation panels now show total # of mutations AND fractional % of a given type (e.g. missense)

New search feature, enabling one to see into which clusters/panels/etc a given patient (or set of patients) falls

After extensive testing, upgraded backend database from Mongo2.x to Mongo3.x: v3 dramatically reduces the memory footprint and data storage sizes, which yields greater performance and also clears considerable breathing room to add more data APIs (e.g. for methylation, RPPA, etc) as well as AWG-specific databases

To address this viewGene issue, insert gene name into metadata to ensure cache is suitably invalidated.

Addressed a performance issue that had crept into the FireBrowse landing page: the sample counts barchart was noticeably slow to load, apparently since mid-August due to a typo in the font name. Strangely, the typo has been there all along, but the landing page has only been slow for about 1 week. It is fast again.

1.1.5 beta (2015_05_11)

iCoMut: a powerful new synoptic tool for interpretation and exploration CoMut figures have quickly become a staple of TCGA research. Within a single graphic they provide a comprehensive analysis profile, enabling the reader to quickly infer relationships between co-occurring results. With iCoMut researchers can now explore coMut figures interactively, sorting and reordering samples and results as they see fit.

New viewGene expression visualizer: built on top of the FireBrowse RESTful API, viewGene generates a boxplot of mRNASeq expression levels for a selected gene across all cohorts.

The fbget suite of automatically-generated, open source wrappers to the FireBrowse RESTful API. fbget makes it even easier to ask both coarse- and fine-grained questions about TCGA data and Firehose analyses, from Python and the UNIX command line.

Reports and FeatureTable apis now make older results available, too, not merely those from the latest analysis run. The search criterion is YYYY_MM_DD datestamp.

We are also very happy to mention FireBrowseR, a set of open source R bindings to FireBrowse developed by a computer science Ph.D. student in Germany!